Created
October 25, 2022 20:52
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Batch renaming + download of several files in google cloud. This was needed because, when downloading with the gcloud CLI (as opposed to the web interface) google just saves the file as "final.vcf" without the full gs:// path. So, trying to batch download a dozen final.vcf files doesn't work.
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| import os | |
| vcfs = ["gs://your_bucket_here/call-varcall/shard-1/var_call_SRR1049633/final.vcf", "gs://your_bucket_here/call-varcall/shard-2/var_call_SRR1049634/final.vcf", "gs://your_bucket_here/call-varcall/shard-3/var_call_SRR1062904/final.vcf", "gs://your_bucket_here/call-varcall/shard-4/var_call_SRR1140590/final.vcf", "gs://your_bucket_here/call-varcall/shard-5/var_call_SRR1047996/final.vcf", "gs://your_bucket_here/call-varcall/shard-6/var_call_SRR1144759/final.vcf", "gs://your_bucket_here/call-varcall/shard-7/var_call_SRR1165658/final.vcf", "gs://your_bucket_here/call-varcall/shard-8/var_call_SRR1167377/final.vcf", "gs://your_bucket_here/call-varcall/shard-9/var_call_SRR1169242/final.vcf"] | |
| new_vcfs = [] | |
| for vcf in vcfs: | |
| split = vcf.split("/") | |
| new_name_start = "/".join(split[:-1])+"/" | |
| new_name_end = split[-2:][0] + ".vcf" | |
| new_name = "".join([new_name_start, new_name_end]) | |
| new_vcfs.append(new_name) | |
| os.system(f"gsutil mv {vcf} {new_name_start}{new_name_end}") | |
| os.system(f"gsutil cp {new_name_start}{new_name_end} .") |
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